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When there is a transmission failure, you can't flush a stacked plate cooler. The stacked plate design has multiple flow paths and the flush will take the past of least resistance and not get the crap out. These coolers will also tend to trap more crap.
If it were a tube and fin cooler then a flush works better. With a stacked plate like these, just don't do it.
If you want to go the cheap route, you can flush the lines and the cooler in the radiator if you want to, but NEVER try that with the stock auxilliary cooler unless you want to go through it all over again.
I replaced it with a new ford one. Got it back and 5 miles later had to take it back cause they didnt put the dip stick tube in right. It didnt seal. But I got the new cooler so I should be all set tomorrow